“…Phaser cells encoded space by assigning distinct phases to allocentric isocontour levels of each cell’s spatial firing pattern. …”
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“…Overall, V-Phaser achieved >97% sensitivity and >97% specificity on control read sets. …”
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“…Variance-refinement functionality was added to Phaser to enable determination of the effective r.m.s.d. that optimized the log-likelihood gain (LLG) for a correct MR solution. …”
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“…The Korean Centers for Disease Control and Prevention (KCDC) developed the Public Health Assessment for Emergency Response (PHASER) Toolkit which was optimized for a weather disaster in Korea. …”
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“…ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. …”
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“…To accomplish this, we chose two leading tools in the field, PHASER and MOLREP. REMO22, along with MOLREP and PHASER, were included in pipelines that contain two additional steps: phase refinement (SYNERGY) and automated model building (CAB). …”
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“…Phaser identified a total of 144 frameshift loci of which 105 were shown to have a statistically significant non-random distribution in phase status. …”
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“…Better sampling is attempted through model trimming or decomposition into rigid groups and optimization through Phaser’s gyre refinement. Also, after model translation, packing filtering and refinement, models are either disassembled into predetermined rigid groups and refined (gimble refinement) or Phaser’s LLG-guided pruning is used to trim the model of residues that are not contributing signal to the LLG at the target r.m.s.d. value. …”
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“…ARCIMBOLDO solves the phase problem by combining the location of small model fragments using Phaser with density modification and autotracing using SHELXE. …”
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“…To encourage ongoing validation of this putative biomarker in diverse populations, diseases, and experimental designs, we developed SkinPhaser––a user-friendly app to test biomarker performance in datasets (https://github.com/gangwug/SkinPhaser).…”
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“…The relationship of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.…”
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“…Test studies have been conducted on five crystal structures of large molecular assemblies, in which EM maps are used as models for structure solution by molecular replacement (MR) using various standard MR packages such as AMoRe, MOLREP and Phaser. The results demonstrate that EM maps are viable models for molecular replacement. …”
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“…An appendix introduces com­bined real–imaginary log-likelihood gradient map coefficients for SAD phasing and their use for substructure completion as implemented in the software Phaser. Supplementary material includes animated probabilistic Harker diagrams showing how maximum-likelihood-based phasing methods can be used to refine parameters in the case of SIR and MIR; it is hoped that these will be useful for those teaching best practice in experimental phasing methods.…”
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“…Initial solutions produced by Phaser after only 5 min perform surprisingly well, improving the prospects for in situ structure solution by AMPLE during synchrotron visits. …”
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“…Descriptions are given of the maximum-likelihood gyre method implemented in Phaser for optimizing the orientation and relative position of rigid-body fragments of a model after the orientation of the model has been identified, but before the model has been positioned in the unit cell, and also the related gimble method for the refinement of rigid-body fragments of the model after positioning. …”
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“…In this manuscript we propose a hybrid Visible Light Communication and Radio Frequency (VLC-RF) scheme for the implementation of a portable Phaser Measurement Unit (PMU) for deep underground tunnels. …”
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“…To cope with such cases, new likelihood approaches have been developed and implemented in Phaser to account for the statistical effects of tNCS in molecular replacement. …”
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“…This paper presents a new pipeline, named Fragon, in which fragments (ideal α-helices or β-strands) are placed using Phaser and the phases calculated from these coordinates are then improved by the density-modification methods provided by ACORN. …”
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“…In a first systematic exploration of phasing with Rosetta de novo models, it is shown that all-atom refinement of coarse-grained models significantly improves both the model quality and performance in molecular replacement with the Phaser software. 15 new cases of diffraction data sets that are unambiguously phased with de novo models are presented. …”
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“…The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. …”
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